The propaganda Japan used during World War 2 when conquering China and Southeast Asia was Greater East Asia Co-Prosperity Sphere
. I suppose that to mean that they would want to be seen as a liberator, one who liberated the native inhabitants from the European forces, and not as a brutal conqueror.

But Japan also committed a lot of atrocities in China and other parts of Southeast Asia after the "liberation". My question is why the generals and officers didn't stop the atrocities, even though such acts would definitely turn the tide of opinion against them, and help contribute to the resistance and the cost of occupation?

Some problems with premise: 1) Not obvious why co-prosperity sphere equals "liberators" - it's co-"prosperity" by being captive markets / resource colonies; 2) No reason to believed Japanese field commanders cared about native opinion more than perceived military value of brutal anti-guriilla operations; 3) Not always a native opinion to turn , e.g. China was anti-Japan right from the start; 4) Dubious assumption that Japanese strategic thinkers could restrain field units even if they wanted to - orders Tokyo issued against marching on Nanking were brazenly ignored by commanders on the ground.
– Semaphore♦Jun 14 '18 at 6:25

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What has your research shown? A brief review of Japanese imperial history would indicate that "the tide of opinion" was not part of their evaluation criteria. They had a very different vision. If I were to research this, I'd start by understanding the Japanese justification for these acts (I don't believe that they perceived them as atrocities, and that they were justified by their perception of the future they were creating).
– Mark C. Wallace♦Jun 14 '18 at 10:00

It would also be useful to document the atrocities - I think it is now commonly accepted that Japan committed atrocities, but discussion of specifics may be more useful than discussion of broad assertions.
– Mark C. Wallace♦Jun 14 '18 at 10:23

1 Answer
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In China, Japan's war was not formally for liberation (China was not a colony), but was simply to punish the Chinese. Japan believed that they were the sole Great Power in the region and that they had the right to defend their interests in Manchuria. Younger officers, whose image of China was highly colored by racism, felt sure that China could not hold out long against Japanese attack, and that their hubris at the Manchurian border deserved punishment. In fact the Chinese Republican army was steadily gaining in power, and from the Chinese perspective Manchuria was being occupied and Japan had no right to be there. The 1937 war was explicitly punitive in nature and Chinese rebels had already been considered subhuman for half a decade, so it's not surprising that although big hearted theorists of the "co-prosperity sphere" called for gentle treatment, the Japanese soldiers were given free reign on the ground.

In Southeast Asia, Japan had a problem familiar to all unwelcome occupiers of that region. While the philosophical plan was for liberation, in practice they were not bringing anything with them but force, and natives knew the difficult terrain much better than them. Japan needed to extract resources from occupied regions and needed to subdue resistance at any cost. The amount of sheer massacre committed in the name of liberation has parallels to the Indonesian occupation of East Timor and the American occupation of the Philippines.

As described in the comments underneath the question, the Japanese army was unprepared for a liberation war in many ways, including a culture of corporal punishment within the army that would be considered brutal and criminal today. There were official attempts at propagandizing which had some effect on intellectuals, but ordinary peasants on the ground were much more viscerally affected by Japanese tendency towards brutality.